Simple analysis of phylogeny using DNA / protein seq data

Evolutionists,
From your experience, do you know whether software such as MacClade
can handle DNA or AA sequence data? I would like to present some simple
ideas about phylogeny, evolution, distance between species etc. to my
freshman biology classes. Is there a preferred way to use seq. data to
demonstrate how far-removed are various species from some common ancesteral
gene or protein?
For example, I have a reference that compares the cytochrome c gene
of 15 species. It lists _how many bases differ_ in the gene for
each species vs. every other species, for a total of 105 comparisons.
Can MacClade generate trees (or other output) that will help me explain
the importance of selection pressure at the molecular level?
The software is reasonably priced, and I'll buy it if it's appropriate
for this kind of purpose.
Thanks in advance for your thoughts. Note that I'm a toxicologist with
only slightly more experience in this area than my students :)
Perhaps I need to read-up a bit more before I can even pose the right
questions...
Scott Knowles < nEcho at NCSUMVS >
North Carolina State University